fn() longestCommonSubsequence
Computes the longest common subsequence.

Defined in <seqan/graph_algorithms.h>
Signature void longestCommonSubsequence(str1, str2, nSize, pos);


str1 An arbitrary ContainerConcept object.
str2 A second arbitrary ContainerConcept object.
nSize The neighbourhood size to use.
pos A String with pairs of positions that indicate the longest common subsequence.

Detailed Description


#include <iostream>
#include <seqan/graph_algorithms.h>
#include <seqan/graph_align.h>

using namespace seqan;

int main()
    // Define two sequences.
    String<char> seq1("abacx");
    String<char> seq2("baabca");

    // Build a StringSet with two elements and an AlignmentGraph over them.
    typedef StringSet<String<char>, Dependent<> > TStringSet;
    TStringSet string_set;
    appendValue(string_set, seq1);
    appendValue(string_set, seq2);
    Graph<Alignment<TStringSet> > alignment_graph(string_set);

    // Compute the longest common subsequence.
    std::cout << "Score = " << globalAlignment(alignment_graph, stringSet(alignment_graph), Lcs()) << "\n"
              << alignment_graph << std::endl;
    return 0;
Score = 3
Alignment matrix:
      0     .
         ||  |

Data Races

Thread safety unknown!

See Also